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RPOA_LDVP
ID   RPOA_LDVP               Reviewed;        3616 AA.
AC   Q83017; Q83018; Q83024; Q83025; Q86716;
DT   12-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT   12-APR-2005, sequence version 2.
DT   03-AUG-2022, entry version 129.
DE   RecName: Full=Replicase polyprotein 1ab;
DE   AltName: Full=ORF1ab polyprotein;
DE   Contains:
DE     RecName: Full=Nsp1-alpha papain-like cysteine proteinase;
DE              EC=3.4.22.-;
DE     AltName: Full=PCP1-alpha;
DE   Contains:
DE     RecName: Full=Nsp1-beta papain-like cysteine proteinase;
DE              EC=3.4.22.-;
DE     AltName: Full=PCP1-beta;
DE   Contains:
DE     RecName: Full=Nsp2 cysteine proteinase;
DE              EC=3.4.22.-;
DE     AltName: Full=CP2;
DE              Short=CP;
DE   Contains:
DE     RecName: Full=Non-structural protein 3;
DE              Short=Nsp3;
DE   Contains:
DE     RecName: Full=3C-like serine proteinase;
DE              Short=3CLSP;
DE              EC=3.4.21.-;
DE     AltName: Full=Nsp4;
DE   Contains:
DE     RecName: Full=Non-structural protein 5-6-7;
DE              Short=Nsp5-6-7;
DE   Contains:
DE     RecName: Full=Non-structural protein 5;
DE              Short=Nsp5;
DE   Contains:
DE     RecName: Full=Non-structural protein 6;
DE              Short=Nsp6;
DE   Contains:
DE     RecName: Full=Non-structural protein 7-alpha;
DE              Short=Nsp7-alpha;
DE   Contains:
DE     RecName: Full=Non-structural protein 7-beta;
DE              Short=Nsp7-beta;
DE   Contains:
DE     RecName: Full=Non-structural protein 8;
DE              Short=Nsp8;
DE   Contains:
DE     RecName: Full=RNA-directed RNA polymerase;
DE              Short=Pol;
DE              Short=RdRp;
DE              EC=2.7.7.48;
DE     AltName: Full=Nsp9;
DE   Contains:
DE     RecName: Full=Helicase;
DE              Short=Hel;
DE              EC=3.6.4.12;
DE              EC=3.6.4.13;
DE     AltName: Full=Nsp10;
DE   Contains:
DE     RecName: Full=Uridylate-specific endoribonuclease nsp11;
DE              EC=4.6.1.-;
DE     AltName: Full=Non-structural protein 11;
DE              Short=Nsp11;
DE   Contains:
DE     RecName: Full=Non-structural protein 12;
DE              Short=Nsp12;
GN   Name=rep; ORFNames=1a-1b;
OS   Lactate dehydrogenase elevating virus (strain Plagemann) (LDV).
OC   Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC   Nidovirales; Arnidovirineae; Arteriviridae; Variarterivirinae;
OC   Gammaarterivirus; Gammaarterivirus lacdeh.
OX   NCBI_TaxID=300016;
OH   NCBI_TaxID=10092; Mus musculus domesticus (western European house mouse).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=7778295; DOI=10.1006/viro.1995.1296;
RA   Palmer G.A., Kuo L.L., Chen Z., Faaberg K.S., Plagemann P.G.W.;
RT   "Sequence of the genome of lactate dehydrogenase-elevating virus:
RT   heterogenicity between strains P and C.";
RL   Virology 209:637-642(1995).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-57.
RX   PubMed=7512122; DOI=10.1099/0022-1317-75-4-925;
RA   Chen Z., Faaberg K.S., Plagemann P.G.W.;
RT   "Determination of the 5' end of the lactate dehydrogenase-elevating virus
RT   genome by two independent approaches.";
RL   J. Gen. Virol. 75:925-930(1994).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 769-1187 AND 2307-2846.
RX   PubMed=1870216; DOI=10.1128/jvi.65.9.5118-5123.1991;
RA   Kuo L.L., Harty J.T., Erickson L., Palmer G.A., Plagemann P.G.W.;
RT   "A nested set of eight RNAs is formed in macrophages infected with lactate
RT   dehydrogenase-elevating virus.";
RL   J. Virol. 65:5118-5123(1991).
RN   [4]
RP   ACTIVE SITES OF PCP1-ALPHA AND PCP1-BETA, AND MUTAGENESIS OF CYS-76 AND
RP   CYS-269.
RX   PubMed=7769711; DOI=10.1128/jvi.69.7.4500-4505.1995;
RA   den Boon J.A., Faaberg K.S., Meulenberg J.J.M., Wassenaar A.L.M.,
RA   Plagemann P.G.W., Gorbalenya A.E., Snijder E.J.;
RT   "Processing and evolution of the N-terminal region of the arterivirus
RT   replicase ORF1a protein: identification of two papainlike cysteine
RT   proteases.";
RL   J. Virol. 69:4500-4505(1995).
CC   -!- FUNCTION: The replicase polyprotein 1ab is a multifunctional protein:
CC       it contains the activities necessary for the transcription of negative
CC       stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as
CC       well as proteinases responsible for the cleavage of the polyprotein
CC       into functional products.
CC   -!- FUNCTION: The Nsp1 chain is essential for viral subgenomic mRNA
CC       synthesis. {ECO:0000250}.
CC   -!- FUNCTION: The 3C-like serine proteinase chain is responsible for the
CC       majority of cleavages as it cleaves the C-terminus of the polyprotein.
CC       {ECO:0000250}.
CC   -!- FUNCTION: The helicase chain, which contains a zinc finger structure,
CC       displays RNA and DNA duplex-unwinding activities with 5' to 3'
CC       polarity. {ECO:0000250}.
CC   -!- FUNCTION: [Uridylate-specific endoribonuclease nsp11]: Plays a role in
CC       viral transcription/replication and prevents the simultaneous
CC       activation of host cell dsRNA sensors, such as MDA5/IFIH1, OAS, and PKR
CC       (By similarity). Acts by degrading the 5'-polyuridines generated during
CC       replication of the poly(A) region of viral genomic and subgenomic RNAs.
CC       Catalyzes a two-step reaction in which a 2'3'-cyclic phosphate (2'3'-
CC       cP) is first generated by 2'-O transesterification, which is then
CC       hydrolyzed to a 3'-phosphate (3'-P) (By similarity). If not degraded,
CC       poly(U) RNA would hybridize with poly(A) RNA tails and activate host
CC       dsRNA sensors (By similarity). {ECO:0000250|UniProtKB:P0C6X7,
CC       ECO:0000250|UniProtKB:P19811}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC         RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC         COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC         EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC   -!- CATALYTIC ACTIVITY: [Uridylate-specific endoribonuclease nsp11]:
CC       Reaction=uridylyl-uridylyl-ribonucleotide-RNA = a 3'-end uridylyl-
CC         2',3'-cyclophospho-uridine-RNA + a 5'-end dephospho-ribonucleoside-
CC         RNA; Xref=Rhea:RHEA:67732, Rhea:RHEA-COMP:13936, Rhea:RHEA-
CC         COMP:17334, Rhea:RHEA-COMP:17335, ChEBI:CHEBI:138284,
CC         ChEBI:CHEBI:173079, ChEBI:CHEBI:173080;
CC         Evidence={ECO:0000250|UniProtKB:P19811};
CC   -!- SUBCELLULAR LOCATION: [Nsp2 cysteine proteinase]: Host membrane
CC       {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Non-structural protein 3]: Host membrane
CC       {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Non-structural protein 5-6-7]: Host membrane
CC       {ECO:0000305}; Multi-pass membrane protein {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [3C-like serine proteinase]: Host cytoplasm
CC       {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [RNA-directed RNA polymerase]: Host cytoplasm,
CC       host perinuclear region {ECO:0000305}.
CC   -!- SUBCELLULAR LOCATION: [Helicase]: Host cytoplasm, host perinuclear
CC       region {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Ribosomal frameshifting; Named isoforms=2;
CC       Name=Replicase polyprotein 1ab; Synonyms=pp1ab;
CC         IsoId=Q83017-1; Sequence=Displayed;
CC       Name=Replicase polyprotein 1a; Synonyms=pp1a, ORF1a polyprotein;
CC         IsoId=Q83017-2; Sequence=VSP_032889;
CC   -!- DOMAIN: The hydrophobic domains (HD) could mediate the membrane
CC       association of the replication complex and thereby alter the
CC       architecture of the host cell membrane. {ECO:0000250}.
CC   -!- PTM: Specific enzymatic cleavages in vivo by its own proteases yield
CC       mature proteins. There are two alternative pathways for processing.
CC       Either nsp4-5 is cleaved, which represents the major pathway or the
CC       nsp5-6 and nsp6-7 are processed, which represents the minor pathway.
CC       The major pathway occurs when nsp2 acts as cofactor for nsp4 (By
CC       similarity). {ECO:0000250}.
CC   -!- MISCELLANEOUS: [Isoform Replicase polyprotein 1ab]: Produced by -1
CC       ribosomal frameshifting at the 1a-1b genes boundary.
CC   -!- MISCELLANEOUS: [Isoform Replicase polyprotein 1a]: Produced by
CC       conventional translation. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the arteriviridae polyprotein family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA85664.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; U15146; AAA85663.1; -; Genomic_RNA.
DR   EMBL; U15146; AAA85664.1; ALT_INIT; Genomic_RNA.
DR   EMBL; S69379; AAB30448.1; -; Genomic_RNA.
DR   EMBL; S50064; AAB19478.1; -; mRNA.
DR   EMBL; S50068; AAB19479.1; -; mRNA.
DR   PIR; B40901; B40901.
DR   PIR; C40901; C40901.
DR   PIR; JQ1998; JQ1998.
DR   PIR; PQ0618; PQ0618.
DR   SMR; Q83017; -.
DR   MEROPS; C31.001; -.
DR   PRIDE; Q83017; -.
DR   GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0044220; C:host cell perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR   GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR   GO; GO:0003678; F:DNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
DR   GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0004252; F:serine-type endopeptidase activity; IEA:InterPro.
DR   GO; GO:0070008; F:serine-type exopeptidase activity; IEA:InterPro.
DR   GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR   GO; GO:0019082; P:viral protein processing; IEA:InterPro.
DR   GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR   CDD; cd21410; 1B_av_Nsp10-like; 1.
DR   CDD; cd21160; NendoU_av_Nsp11-like; 1.
DR   CDD; cd21166; NTD_av_Nsp11-like; 1.
DR   CDD; cd21405; ZBD_av_Nsp10-like; 1.
DR   Gene3D; 2.40.10.10; -; 2.
DR   Gene3D; 3.30.1330.220; -; 1.
DR   Gene3D; 3.30.40.20; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   Gene3D; 3.90.70.60; -; 1.
DR   Gene3D; 3.90.70.70; -; 1.
DR   InterPro; IPR027351; (+)RNA_virus_helicase_core_dom.
DR   InterPro; IPR031932; Arteri_nsp7a.
DR   InterPro; IPR038451; Arteri_nsp7a_sf.
DR   InterPro; IPR008743; Arterivirus_Nsp2_C33.
DR   InterPro; IPR023338; Arterivirus_NSP4_peptidase.
DR   InterPro; IPR008741; AV_PCPalpha.
DR   InterPro; IPR038155; AV_PCPalpha_sf.
DR   InterPro; IPR025773; AV_PCPbeta.
DR   InterPro; IPR038154; AV_PCPbeta_sf.
DR   InterPro; IPR023183; Chymotrypsin-like_C.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR022230; DUF3756.
DR   InterPro; IPR008760; EAV_peptidase_S32.
DR   InterPro; IPR037227; EndoU-like.
DR   InterPro; IPR044863; NIRAN.
DR   InterPro; IPR044348; NSP10_1B_Av.
DR   InterPro; IPR027355; NSP10_Av_ZBD.
DR   InterPro; IPR044320; NSP11_Av_N.
DR   InterPro; IPR044314; NSP11_NendoU_Av.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR009003; Peptidase_S1_PA.
DR   InterPro; IPR043504; Peptidase_S1_PA_chymotrypsin.
DR   InterPro; IPR001205; RNA-dir_pol_C.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   Pfam; PF16749; Arteri_nsp7a; 1.
DR   Pfam; PF12581; DUF3756; 1.
DR   Pfam; PF05410; Peptidase_C31; 1.
DR   Pfam; PF05411; Peptidase_C32; 1.
DR   Pfam; PF05412; Peptidase_C33; 1.
DR   Pfam; PF05579; Peptidase_S32; 1.
DR   Pfam; PF00680; RdRP_1; 1.
DR   Pfam; PF01443; Viral_helicase1; 1.
DR   SUPFAM; SSF142877; SSF142877; 1.
DR   SUPFAM; SSF50494; SSF50494; 1.
DR   SUPFAM; SSF52540; SSF52540; 2.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS51538; AV_CP; 1.
DR   PROSITE; PS51961; AV_NSP11N_COV_NSP15M; 1.
DR   PROSITE; PS51493; AV_NSP4_PRO; 1.
DR   PROSITE; PS51539; AV_PCP_ALPHA; 1.
DR   PROSITE; PS51540; AV_PCP_BETA; 1.
DR   PROSITE; PS51652; AV_ZBD; 1.
DR   PROSITE; PS51958; NENDOU; 1.
DR   PROSITE; PS51947; NIRAN; 1.
DR   PROSITE; PS51657; PSRV_HELICASE; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Helicase; Host cytoplasm; Host membrane; Hydrolase; Lyase;
KW   Membrane; Metal-binding; Nucleotide-binding; Nucleotidyltransferase;
KW   Protease; Ribosomal frameshifting; RNA-directed RNA polymerase;
KW   Serine protease; Thiol protease; Transferase; Transmembrane;
KW   Transmembrane helix; Viral RNA replication; Zinc; Zinc-finger.
FT   CHAIN           1..3616
FT                   /note="Replicase polyprotein 1ab"
FT                   /id="PRO_0000036644"
FT   CHAIN           1..?
FT                   /note="Nsp1-alpha papain-like cysteine proteinase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036646"
FT   CHAIN           ?..380
FT                   /note="Nsp1-beta papain-like cysteine proteinase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036647"
FT   CHAIN           381..1286
FT                   /note="Nsp2 cysteine proteinase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036648"
FT   CHAIN           1287..1512
FT                   /note="Non-structural protein 3"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036649"
FT   CHAIN           1513..1714
FT                   /note="3C-like serine proteinase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036650"
FT   CHAIN           1715..2161
FT                   /note="Non-structural protein 5-6-7"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036651"
FT   CHAIN           1715..1878
FT                   /note="Non-structural protein 5"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000423114"
FT   CHAIN           1879..1894
FT                   /note="Non-structural protein 6"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000423115"
FT   CHAIN           1895..2026
FT                   /note="Non-structural protein 7-alpha"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000423116"
FT   CHAIN           2027..2161
FT                   /note="Non-structural protein 7-beta"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000423117"
FT   CHAIN           2162..2843
FT                   /note="RNA-directed RNA polymerase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036652"
FT   CHAIN           2162..2206
FT                   /note="Non-structural protein 8"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036653"
FT   CHAIN           2844..3272
FT                   /note="Helicase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036654"
FT   CHAIN           3273..3494
FT                   /note="Uridylate-specific endoribonuclease nsp11"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036655"
FT   CHAIN           3495..3616
FT                   /note="Non-structural protein 12"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000036656"
FT   TRANSMEM        942..962
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        977..997
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1010..1030
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1060..1080
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1085..1105
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1289..1309
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1364..1384
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1386..1406
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1425..1445
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1715..1735
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1737..1757
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1761..1781
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   TRANSMEM        1832..1852
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   DOMAIN          69..181
FT                   /note="Peptidase C31"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00872"
FT   DOMAIN          262..381
FT                   /note="Peptidase C32"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00873"
FT   DOMAIN          381..486
FT                   /note="Peptidase C33"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00871"
FT   DOMAIN          1513..1714
FT                   /note="Peptidase S32"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00826"
FT   DOMAIN          2194..2352
FT                   /note="NiRAN"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01292"
FT   DOMAIN          2590..2724
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   DOMAIN          2844..2907
FT                   /note="AV ZBD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   DOMAIN          2964..3116
FT                   /note="(+)RNA virus helicase ATP-binding"
FT   DOMAIN          3117..3248
FT                   /note="(+)RNA virus helicase C-terminal"
FT   DOMAIN          3272..3368
FT                   /note="AV-Nsp11N/CoV-Nsp15M"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01306"
FT   DOMAIN          3370..3492
FT                   /note="NendoU"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01303"
FT   ZN_FING         8..28
FT                   /note="C4-type; atypical"
FT   REGION          672..706
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          883..912
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          981..1105
FT                   /note="HD1"
FT   REGION          1289..1448
FT                   /note="HD2"
FT   REGION          1737..1852
FT                   /note="HD3"
FT   ACT_SITE        76
FT                   /note="For Nsp1-alpha papain-like cysteine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00872,
FT                   ECO:0000269|PubMed:7769711"
FT   ACT_SITE        147
FT                   /note="For Nsp1-alpha papain-like cysteine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00872,
FT                   ECO:0000269|PubMed:7769711"
FT   ACT_SITE        269
FT                   /note="For Nsp1-beta papain-like cysteine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00873,
FT                   ECO:0000269|PubMed:7769711"
FT   ACT_SITE        340
FT                   /note="For Nsp1-beta papain-like cysteine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00873,
FT                   ECO:0000269|PubMed:7769711"
FT   ACT_SITE        390
FT                   /note="For Nsp2 cysteine proteinase activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00871"
FT   ACT_SITE        456
FT                   /note="For Nsp2 cysteine proteinase activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00871"
FT   ACT_SITE        1551
FT                   /note="Charge relay system; for 3C-like serine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00826"
FT   ACT_SITE        1576
FT                   /note="Charge relay system; for 3C-like serine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00826"
FT   ACT_SITE        1628
FT                   /note="Charge relay system; for 3C-like serine proteinase
FT                   activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00826"
FT   BINDING         2850
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2853
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2863
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2868
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2871
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2873
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2875
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2877
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2884
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2886
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2893
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2896
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00985"
FT   BINDING         2992..2999
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   SITE            181..182
FT                   /note="Cleavage; by autolysis"
FT                   /evidence="ECO:0000255"
FT   SITE            381..382
FT                   /note="Cleavage; by autolysis"
FT                   /evidence="ECO:0000255"
FT   SITE            1286..1287
FT                   /note="Cleavage; by CP2"
FT                   /evidence="ECO:0000250"
FT   SITE            1512..1513
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            1714..1715
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            1878..1879
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            1894..1895
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            2026..2027
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            2161..2162
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            2843..2844
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            3272..3273
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   SITE            3494..3495
FT                   /note="Cleavage; by 3CLSP"
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         2207..3616
FT                   /note="Missing (in isoform Replicase polyprotein 1a)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_032889"
FT   MUTAGEN         76
FT                   /note="C->S: Complete loss of cleavage between nsp1-alpha
FT                   and nsp1-beta."
FT                   /evidence="ECO:0000269|PubMed:7769711"
FT   MUTAGEN         269
FT                   /note="C->A: Complete loss of cleavage between nsp1-beta
FT                   and nsp2."
FT                   /evidence="ECO:0000269|PubMed:7769711"
FT   CONFLICT        1185
FT                   /note="E -> K (in Ref. 3)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        2748..2753
FT                   /note="SEPKLP -> QNPNFL (in Ref. 3)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        2771..2777
FT                   /note="VAALAYQ -> RRGASVS (in Ref. 3)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        2820..2823
FT                   /note="GSPW -> RKEG (in Ref. 3)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        2843
FT                   /note="E -> K (in Ref. 3)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   3616 AA;  396434 MW;  6167A231CDE7B611 CRC64;
     MQSGFDRCLC TPNARVFWEH GQVYCTRCLA ARPLLPLSQQ NPRLGALGLF YRPATPLTWE
     APITYPTKEC RPGGLCWLSG IYPIARMTSG NHNFQARLNF VASVVYRDGK LTSKHLEEEF
     EVYSRGCRWY PITGPVPGIA LYANAVHVSD EPFPGCTHVL SNLPLPQQPL RKGLCPFSDA
     RAEVWRYKGN TIFVSEQGYL WTTGSNDSVP EPWGEARRLC EKIIASLPAD HLVKIEFSNY
     PFDYSFTGGD GAGYVLFPCK KNDTKFSKCW EKVFEDHSSW KVACEEADLA DRMGYRTPAG
     VAGPYLARRL QYRGLRAVVK PEQNDYVVWA LGVPESYIRH ISRAGEPVEN FFVRVGEFSI
     VSNCVATPYP KFRFQTRKYY GYSPPGDGAC GLHCISAIIN DIFGDALCTK LTNCSRDSSE
     WLSDQDMYQL VMTARLPATL GHCPSATYKL DCVNQHWTVT KRKGDRALGG LSPECVRGVC
     GGECKFVPTY PREINLELAA KSPISALAFS LGVEPYCDCW NFTNSVLVND SLAVETARAG
     EAYRSAMGIP KDDWVLLAEL MTENCLTRRE VLDKLQRGLR LHATSKPGSP ASVSPASSID
     FSAAGLLLDG TESDKEAVVA VNNDCYTVLG FDKNSATKSE QELATGLFSE LVEPMETSTS
     KHESRKILEA ASRALKSAKP KRKRNKKKKT SSPTPTPPET PTREVPGAIE VVSGDEEAGA
     CESATIVPDK AQARPPPRPK RQALKKAEQG FILKDIIWNP TESGVKCLTI VEDVRAFLKS
     ITPPGGALGT RARITAHIVE QFHVIRESTP ELVLAHAEHQ AKNMHELLLS EKAKLILGIG
     EDTLKKLVSS QRSLPRSIGF GAWLSDQQKT ADSCGEREFV EVPLKSGAEP TPSKRDLGVS
     LGDQLSQDGA PRLSSSTACE IKERVPPIKD SGGGLGQKFM AWLNHQVFLL SSHLLAMWSV
     VLGSRQKLNW ADYVYTLFCL CCVLLCFHFP AIGFIPLAGC VFGSPWRVRL SVFSVWLCVA
     VVVFQEVLPE PGSVCSSASA ECAAALERYS GNGVHRPVNH IGVGLVGTVA GFVARVVGGP
     RHYWFYFLRL MVVLDLGLVF LAVALRGRCK KCFCKCVRVA PHEVHLRVFP LTKVARPTLE
     AVCDMYSAPR VDPILVATGI KGCWQGKVSP HQVTDKPVSY SNLEEKKISN KTVVPPPTDP
     QQAVKCLKVL QCGGSIQDVG VPEVKKVSKV PYKAPFFPNV SIDPECYIVV DPVTYSAAMR
     GGYGVSHLIV GTGDFAEVNG LRFVSGGHVA DFVCLGLYVM LNFLISAWLS SPVSCGRGTN
     DPWCKNPFSY PVVGQGVMCN SHLCISEDGL TSPMVLSYSL IDWALMIAVI ATVAIFIAKV
     SLLVDVICVF LCLLMYVFPP LSVIAFAFPF ALCKVHLHPV TLVWVQFFLL AVNFWAGVAV
     AVILISSWFL ARATSSTGLV TPYDVHLVTS TPRGASSLAS APEGTYLAAV RRSALTGRCC
     MFVPTNFGSV LEGSLRTRGC AKNVVSVFGS ASGSGGVFTI HGNPVVVTAT HLLSDGKARV
     SCVGFSQCLT FKSVGDYAFA RVAEWKGDAP KVELSDRRGR AYCSPQVEWS LVLLGPNTAF
     CFTKCGDSGS PVVDEDGNLI GVHTGSNKRG SGMITTHNGK TLGMSNVKLS EMCQHYGGSG
     VPVSTVRLPK HLIVDVEAVA SDLVAVVESL PTPEGALSSV QLLCVFFFLW RLIHVPFVPV
     IAVAFFFLNE ILPVVLARLM FSFALSLFSV FTGFSVQVLL LRLVIAALNR SAVSFGSFLL
     GQLFHCCLMP SHLETLGPVP GYFYPSTTEV ASKEIFVTLL AIHVLALLLS LFKRPMLADV
     LVGNGSFDAA FFLKYFAEGN LRDGVSDSCN MTPEGLTAAL AITLSDDDLE FLQRHSEFKC
     FVSASNMRNG AKEFIESAYA RALRAQLAAT DKIKASKSIL AKLESFAGGV VTKVEPGDVV
     VVLGKKIVGD LVEITINDVK HVIRVIETRV MAGTQFSVGT ICGDLENACE DPSGLVKTSK
     KQRRRQKRTG LGTEVVGTVE IDGVSYNKVW HKATGDVTYE GFLVSENSRL RTLGTSAIGR
     FQEFIRKHGS KVKTSVEKYP VGKNKHIEFA VTTYNLDGEE FDVPDHEPLE WTITIGDSDL
     EAERLTVDQA LRHMGHDSLL TPKEKEKLAR IIESLNGLQQ SSALNCLTTS GLERCSRGGV
     TVSKDAVKIV KYHSRTFSIG DVNLKVMSFD EYRRTMGKPG HLLVAKLTDG VVVMRKHEPS
     LVDVILTGED AEFFPRTHGP GNTGIHRFVW DFESPPVDLE LELSEQIITA CSMRRGDAPA
     LDLPYKLHPV RGDPYRHRGV LFNTRFGDIT YLIPEKTKEP LHAAACYNKG VPVSDSETLV
     ATTLPHGFEL YVPTLPPSVL EYLDSRPDTP RMLTKHGCAS AAEKDLQKFD LSRQGFVLPG
     VLYMVRRYLS RLIGVRRRLF MPSTYPAKNS MAGINGGRFP LTWLQSHPDI DALCKRACEE
     HWQTVTPCTL KKQYCSKSKT RTILGTNNFV ALGLRSALSG VTQGFMRKGI GTPICLGKNK
     FTPLPVRIGG RCLEADLASC DRSTPAIIRW FTTNLLFELA GAEEWIPSYV LNCCHDVVST
     MSGCFDKRGG LSSGDPVTSI SNTVYSLIIY AQHMVLSAFR CGHKIGGLFL QDSLEMEQLF
     ELQPLLVYSD DVVFYNESDE LPNYHFFVDH LDLMLGFKTD RSKTVITSEP KLPGCRISGG
     RVLVPQRDRI VAALAYQMKA SCVGEYFASA AAILMDACAC CDHDESWYFD LVCGIAECAG
     SPWFRFPGPS FFLDMWNRLS AEEKKKCRTC AHCGAPATLV SSCGLNLCDY HGHGHPHCPV
     VLPCGHAVGS GVCEQCSSSA MNLNTELDIL LMCVPYHPPK VELLSVNDKV SSLPPGAYQA
     RGGVVSVRRD ILGNVVDLPD GDYQVMKVAQ TCADISMVSV NSNILRSQFV TGAPGTGKTT
     YLLSVVRDDD VIYTPTHRTM LDVVKALKVC RFDPPKDTPL EFPVPGRTGP TVRLIGAGFV
     PGRVSYLDEA AYCNPLDVLK VLSKTPLVCV GDLNQLPPVG FNGPCFAFSL MPGRQLIEVF
     RFGPAVVNSI KKFYKEELVP RGPDTGVKFL KQYQPYGQVL TPYHRDRVDG AITIDSSQGC
     TYDVVTVYLP TPKSLNSARA LVALTRARHY VFIYDPYDQL QQYLQVFEHE PADAWAFWCG
     DQPKMIVGGV VKQLAGHSRT TDLKLQQLMG LEGTASPLPQ VGHNLGFYYS PDLIQFAKIP
     PELCKHWPVV TAQNRTEWPD RLVCGMNKMD KNSRAVFCAG YYVGPSIFLG VPGVVSYYLT
     KYLKGESVPL PDSIMSTGRI RLNVREYLDE NEIEFAKKCP QPFIGEVKGS NVGGCHHVTS
     RFLPPVLVPG SVVKVGVSCP GKAAKGLCTV TDVYLPELDS YLHPPSKSMD YKLLVDFQPV
     KLMVWKDATA YFHEGIRPME AMSRFLKVPE GEGVFFDLDE FVTNAKVSKL PCKYSVSAHQ
     FLTEVVLSMT PTSEAPPDYE LLFARAYCVP GLDVGTLNAY IYKRGPSTYT TSNFARLVKD
     TAVPVGCKGS GYMFPK
 
 
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